After the Fair Work Commission last month found the latest ATO workplace deal let it move all staff onto hot desks, the Australian Services Union has lodged an appeal saying the umpire erred and that the agreement prohibited the office fit-outs for non-fieldwork public servants.

ASU official Jeff Lapidos said hot-desking, a controversial workplace trend, was a dramatic change to staff's conditions of employment.

"This type of change needs to be negotiated by the unions and approved by a majority of ATO staff through the enterprise bargaining process. This has not occurred," he said.

"Many types of ATO work are definitely not suitable for hot-desking. If the ATO wants to utilise hot-desking it needs to reach agreement with the unions and its staff about what types of work are appropriate for hot-desking and how it could be implemented.

"There are also issues of inconvenience, hygiene, uncertainty, inability to personalise your desk and many others."

The union would also want to reach agreement with the ATO on the types of desks to be used and the facilities needed to support hot-desking.

Mr Lapidos said it wanted the ATO to negotiate all accommodation measures with unions as part of the 2020 enterprise agreement, so staff could decide whether to support hot-desking, and that if the ASU lost its Fair Work appeal the agency would introduce the new fit-outs to other offices.

Despite arguments from the ASU and the Community and Public Sector Union, Fair Work last month found the enterprise agreement let the ATO move all of its public servants into hot-desking, an office set-up whereby staff find new desks each day and pack up their belongings before finishing.

But the Tax Office, which wants to adopt hot-desking at its new Gosford office and has trialled it at Docklands, said after the decision it had no plans to roll it out in all workplaces.

"Where there is the opportunity in the fit-out of new buildings or refurbishments the ATO will consider how to design spaces in a way that creates a healthy working environment that improves flexibility, agility, collaboration and productivity," a spokeswoman said last month.

The ATO in December said its pilot site for "activity-based working" in Docklands had a waiting list of staff wanting to work there.

"We have many staff across other locations asking for similar work spaces to be installed so we have the type of professional and modern workplaces they see in a large and growing number of other organisations," it said.

The Docklands trial and staff consultation had made the ATO more adaptable to business and staff needs.

"Staff working in this environment have told us they have spent more time sharing their ideas and knowledge and believe they have increased their individual and team productivity."